Article ID: 575 - Last Modified: May 1, 2012

I tried to generate a grid for docking with Glide using the SiteMap output. I got the following warnings. What do they mean?

The input protein structure does not appear to have been prepared with the Protein Preparation Wizard.

WARNING: rdmmct(): Invalid atomic number -2, at atom of mmct 8. Atomtyping, docking will be skipped, other tasks may fail.

Maestro determines if a structure has been prepared based on structure-level properties created during the preparation process. In Suite 2009, SiteMap, did not preserve these properties in its output receptor structure. If you have used the Protein Preparation Wizard to prepare the input structure to SiteMap, you can ignore the warning about the receptor not being prepared, when generating the Glide grid. The preparation properties are passed to the output file as of Suite 2010, so you should no longer see this warning, unless the protein was prepared in an earlier release that does not have these properties.

The Grid Generation error about an invalid atomic
number in the receptor structure could occur if you picked a site point as the ligand while in "Molecule" picking mode, rather than "Entry" picking mode (on the Receptor tab). If you identify a site point as the ligand, then only that individual site point will be extracted from the structure, leaving dummy atoms in the active site which Glide can't handle. Using "Entry" picking mode will cause all site points in that SiteMap output entry to be selected as the 'ligand' and later extracted from the structure.

Keywords:
SiteMap, Glide, warning,

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